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  • ae_ucla
    Member
    • Aug 2010
    • 11
    #1

    Multiple gene entries in cuffdiff output

    Hi, I am using the newest version of cufflinks. My gene_exp.diff output has multiple entries for the same gene.
    Any advice on how to interpret this?
    thanks, my output is below:
    XLOC_018608 Abcc1 chr16:14361656-14474908 q1 q2 OK 55.6561 79.9716 0.362481 -2.36234 0.01816 yes
    XLOC_019036 Abcc1 chr16:14361656-14474908 q1 q2 OK 31.3538 28.6873 -0.0888808 2.38636 0.0170159 yes
    XLOC_019037 Abcc1 chr16:14361656-14474908 q1 q2 OK 16.9886 0 6.95331e-310 2.22507e-308 0 yes
    XLOC_019038 Abcc1 chr16:14361656-14474908 q1 q2 OK 23.4774 11.7544 -0.69181 20.0878 0 yes
    XLOC_019039 Abcc1 chr16:14361656-14474908 q1 q2 OK 4.30056 0.0429869 -4.6056 74.2834 0 yes
    XLOC_019040 Abcc1 chr16:14361656-14474908 q1 q2 OK 20.3121 6.59354 -1.12513 20.2536 0 yes
    XLOC_019041 Abcc1 chr16:14361656-14474908 q1 q2 OK 25.6971 19.676 -0.266978 7.40506 1.31006e-13 yes
    XLOC_019042 Abcc1 chr16:14361656-14474908 q1 q2 OK 18.6257 9.21554 -0.703649 17.9531 0 yes
    XLOC_019043 Abcc1 chr16:14361656-14474908 q1 q2 OK 33.9496 23.3369 -0.37484 12.6007 0 yes
    XLOC_019048 Abcc1 chr16:14361656-14474908 q1 q2 OK 0 8.51373 1.97626e-322 1.79769e+308 0 yes
    XLOC_019049 Abcc1 chr16:14361656-14474908 q1 q2 OK 15.07 9.65164 -0.445577 6.79318 1.09689e-11 yes
    XLOC_019051 Abcc1 chr16:14361656-14474908 q1 q2 OK 18.7229 29.8567 0.466659 -11.2294 0 yes
    XLOC_019053 Abcc1 chr16:14361656-14474908 q1 q2 OK 6.7633 2.70006 -0.918239 9.43042 0 yes
    Tags: cuffdiff, cufflinks
  • ae_ucla
    Member
    • Aug 2010
    • 11
    #2
    Hi, I just wanted to update my previous post. I previously ran cufflinks in the following way, in order to find known and novel transcripts:
    I ran tophat without a reference, ran cufflinks without a reference on each bam file, ran cuffcompare with the ensemble ref and my output gtfs, and then ran cuffdiff on the combined gtf and bam files.
    Since I am mostly interested in known transcripts, I now reran tophat with the ensembl gtf and ran cuffdiff on that output with the ensembl gtf and the bam files.
    I now end up with only one value per gene, so I will use these much clearer results for now.

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